Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

doi:10.1107/S0021889807067908

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Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

Journal Article•DOI•

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

Clare F. Macrae¹, Ian J. Bruno¹, James A. Chisholm¹, Paul R. Edgington¹, Patrick McCabe¹, Elna Pidcock¹, Lucia Rodriguez-Monge¹, Robin Taylor¹, Jacco van de Streek¹, Peter A. Wood¹ - Show less +6 more•Institutions (1)

University of Cambridge¹

01 Apr 2008-Journal of Applied Crystallography (International Union of Crystallography)-Vol. 41, Iss: 2, pp 466-470

TL;DR: Mercury as discussed by the authors is a crystal structure visualization tool that allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns, as well as the ability to perform packing similarity calculations between structures containing the same compound.

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Abstract: The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.

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Journal Article•DOI•

The Cambridge Structural Database

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Colin R. Groom¹, Ian J. Bruno¹, Matthew P. Lightfoot¹, Suzanna C. Ward¹•Institutions (1)

University of Cambridge¹

01 Apr 2016-Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry

TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.

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Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

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6,313 citations

Cites methods from "Mercury CSD 2.0 – new features for ..."

...As well as these services there are a number of other avenues to explore and exploit the data ranging from free lookup tools such as CellCheckCSD (Wood, 2011) to advanced search, analysis and validation tools in the CSD-System (Bruno et al., 1997, 2002, 2004; Macrae et al., 2008)....
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Journal Article•DOI•

Hirshfeld surface analysis

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Mark A. Spackman¹, Dylan Jayatilaka¹•Institutions (1)

University of Western Australia¹

07 Jan 2009-CrystEngComm

TL;DR: In the last few years, the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity as mentioned in this paper, which represents an attempt to venture beyond the current paradigm of nuclear distances and angles, crystal packing diagrams with molecules represented via various models, and to view molecules as organic wholes.

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Abstract: In the last few years the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity. This approach represents an attempt to venture beyond the current paradigm—internuclear distances and angles, crystal packing diagrams with molecules represented via various models, and the identification of close contacts deemed to be important—and to view molecules as “organic wholes”, thereby fundamentally altering the discussion of intermolecular interactions through an unbiased identification of all close contacts.

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4,930 citations

Journal Article•DOI•

Mercury 4.0: from visualization to analysis, design and prediction

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Clare F. Macrae¹, Ioana Sovago¹, Simon J. Cottrell¹, Peter T. A. Galek¹, Patrick McCabe¹, Elna Pidcock¹, Michael Platings¹, Greg P. Shields¹, Joanna S. Stevens¹, Matthew Towler¹, Peter A. Wood¹ - Show less +7 more•Institutions (1)

University of Cambridge¹

01 Feb 2020-Journal of Applied Crystallography

TL;DR: An overview of Mercury 4.0, an analysis, design and prediction platform that acts as a hub for the entire Cambridge Structural Database software suite, is presented.

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Abstract: The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

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2,075 citations

Cites background or methods from "Mercury CSD 2.0 – new features for ..."

...(i) The ‘Motif Search’ component (Macrae et al., 2008) reveals the frequency of occurrence for different motifs involving functional groups of a target molecule....
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...A collection of tools to help interpret and compare packing trends in crystal structures with CSD data using packing feature, similarity and motif searches (Wang et al., 2014) was introduced in Mercury 2.0 (Macrae et al., 2008)....
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...…become established as a prominent crystal structure visualizer with a free-to-access version available for any researcher and many thousands of citations of its first two versions [at the time of writing 4608 for Mercury 1.0 (Macrae et al., 2006) and 5459 for Mercury 2.0 (Macrae et al., 2008)]....
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...This paper in particular will illustrate the evolution of Mercury over the past decade from version 2.0, described by Macrae et al. (2008), up to the recently released version 4.0....
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...In previous versions of Mercury (Macrae et al., 2008), structures and associated parameters from ConQuest searches (Bruno et al., 2002) could be imported and viewed within Mercury....
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Journal Article•DOI•

Idealized powder diffraction patterns for cellulose polymorphs

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Alfred D. French¹•Institutions (1)

United States Department of Agriculture¹

01 Apr 2014-Cellulose

TL;DR: In this paper, powder diffraction patterns from cellulose Iα, Iβ, II, IIII, and IIIII were calculated based on the published atomic coordinates and unit cell dimensions contained in modified "crystal information files" that are supplied in the Supplementary Information.

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Abstract: Cellulose samples are routinely analyzed by X-ray diffraction to determine their crystal type (polymorph) and crystallinity. However, the connection is seldom made between those efforts and the crystal structures of cellulose that have been proposed with synchrotron X-radiation and neutron diffraction over the past decade or so. In part, this desirable connection is thwarted by the use of different conventions for description of the unit cells of the crystal structures. In the present work, powder diffraction patterns from cellulose Iα, Iβ, II, IIII, and IIIII were calculated based on the published atomic coordinates and unit cell dimensions contained in modified “crystal information files” (.cif) that are supplied in the Supplementary Information. The calculations used peak widths at half maximum height of both 0.1 and 1.5° 2θ, providing both highly resolved indications of the contributions of each contributing reflection to the observable diffraction peaks as well as intensity profiles that more closely resemble those from practical cellulose samples. Miller indices are shown for each contributing peak that conform to the convention with c as the fiber axis, a right-handed relationship among the axes and the length of a < b. Adoption of this convention, already used for crystal structure determinations, is also urged for routine studies of polymorph and crystallinity. The calculated patterns are shown with and without preferred orientation along the fiber axis. Diffraction intensities, output by the Mercury program from the Cambridge Crystallographic Data Centre, have several uses including comparisons with experimental data. Calculated intensities from different polymorphs can be added in varying proportions using a spreadsheet program to simulate patterns such as those from partially mercerized cellulose or various composites.

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1,825 citations

Cites background or methods from "Mercury CSD 2.0 – new features for ..."

...The present work is based only on the Mercury 3.0 program, which is available in both free download and full-capability versions (Macrae et al. 2008)....
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...…were based on different sizes of crystals, either from the coordinates of one asymmetric unit in the unit cell, using the Mercury program (Macrae et al. 2008) or from crystal models that had various shapes, sizes and amounts of water or deviation from a perfect lattice that resulted from…...
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...0 program, which is available in both free download and full-capability versions (Macrae et al. 2008)....
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...These calculations were based on different sizes of crystals, either from the coordinates of one asymmetric unit in the unit cell, using the Mercury program (Macrae et al. 2008) or from crystal models that had various shapes, sizes and amounts of water or deviation from a perfect lattice that resulted from molecular dynamics studies....
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Journal Article•DOI•

A Medicinal Chemist’s Guide to Molecular Interactions

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Caterina Bissantz¹, Bernd Kuhn¹, Martin Stahl¹•Institutions (1)

Hoffmann-La Roche¹

26 Mar 2010-Journal of Medicinal Chemistry

TL;DR: This article compile and review the literature on molecular interactions as it pertains to medicinal chemistry through a combination of careful statistical analysis of the large body of publicly available X-ray structure data and experimental and theoretical studies of specific model systems.

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Abstract: Molecular recognition in biological systems relies on the existence of specific attractive interactions between two partner molecules. Structure-based drug design seeks to identify and optimize such interactions between ligands and their host molecules, typically proteins, given their three-dimensional structures. This optimization process requires knowledge about interaction geometries and approximate affinity contributions of attractive interactions that can be gleaned from crystal structure and associated affinity data. Here we compile and review the literature on molecular interactions as it pertains to medicinal chemistry through a combination of careful statistical analysis of the large body of publicly available X-ray structure data and experimental and theoretical studies of specific model systems. We attempt to extract key messages of practical value and complement references with our own searches of the CSDa,(1) and PDB databases.(2) The focus is on direct contacts between ligand and protein functional groups, and we restrict ourselves to those interactions that are most frequent in medicinal chemistry applications. Examples from supramolecular chemistry and quantum mechanical or molecular mechanics calculations are cited where they illustrate a specific point. The application of automated design processes is not covered nor is design of physicochemical properties of molecules such as permeability or solubility. Throughout this article, we wish to raise the readers’ awareness that formulating rules for molecular interactions is only possible within certain boundaries. The combination of 3D structure analysis with binding free energies does not yield a complete understanding of the energetic contributions of individual interactions. The reasons for this are widely known but not always fully appreciated. While it would be desirable to associate observed interactions with energy terms, we have to accept that molecular interactions behave in a highly nonadditive fashion.3,4 The same interaction may be worth different amounts of free energy in different contexts, and it is very hard to find an objective frame of reference for an interaction, since any change of a molecular structure will have multiple effects. One can easily fall victim to confirmation bias, focusing on what one has observed before and building causal relationships on too few observations. In reality, the multiplicity of interactions present in a single protein−ligand complex is a compromise of attractive and repulsive interactions that is almost impossible to deconvolute. By focusing on observed interactions, one neglects a large part of the thermodynamic cycle represented by a binding free energy: solvation processes, long-range interactions, conformational changes. Also, crystal structure coordinates give misleadingly static views of interactions. In reality a macromolecular complex is not characterized by a single structure but by an ensemble of structures. Changes in the degrees of freedom of both partners during the binding event have a large impact on binding free energy. The text is organized in the following way. The first section treats general aspects of molecular design: enthalpic and entropic components of binding free energy, flexibility, solvation, and the treatment of individual water molecules, as well as repulsive interactions. The second half of the article is devoted to specific types of interactions, beginning with hydrogen bonds, moving on to weaker polar interactions, and ending with lipophilic interactions between aliphatic and aromatic systems. We show many examples of structure−activity relationships; these are meant as helpful illustrations but individually can never confirm a rule.

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1,162 citations

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References

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Open Access

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Journal Article•DOI•

Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals

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Joel Bernstein¹, Joel Bernstein², Raymond E. Davis², Liat Shimoni¹, Ning-Leh Chang² - Show less +1 more•Institutions (2)

Ben-Gurion University of the Negev¹, University of Texas at Austin²

18 Aug 1995-Angewandte Chemie

TL;DR: In this article, a review of the most promising systematic approaches to resolving this enigma was initially developed by the late M. C. Etter, who applied graph theory to recognize, and then utilize, patterns of hydrogen bonding for the understanding and design of molecular crystals.

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Abstract: Whereas much of organic chemistry has classically dealt with the preparation and study of the properties of individual molecules, an increasingly significant portion of the activity in chemical research involves understanding and utilizing the nature of the interactions between molecules. Two representative areas of this evolution are supramolecular chemistry and molecular recognition. The interactions between molecules are governed by intermolecular forces whose energetic and geometric properties are much less well understood than those of classical chemical bonds between atoms. Among the strongest of these interactions, however, are hydrogen bonds, whose directional properties are better understood on the local level (that is, for a single hydrogen bond) than many other types of non-bonded interactions. Nevertheless, the means by which to characterize, understand, and predict the consequences of many hydrogen bonds among molecules, and the resulting formation of molecular aggregates (on the microscopic scale) or crystals (on the macroscopic scale) has remained largely enigmatic. One of the most promising systematic approaches to resolving this enigma was initially developed by the late M. C. Etter, who applied graph theory to recognize, and then utilize, patterns of hydrogen bonding for the understanding and design of molecular crystals. In working with Etter's original ideas the power and potential utility of this approach on one hand, and on the other, the need to develop and extend the initial Etter formalism was generally recognized. It with that latter purpose that we originally undertook the present review.

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7,616 citations

"Mercury CSD 2.0 – new features for ..." refers background in this paper

...41, 466–470 Clare F. Macrae et al. Mercury CSD 2.0 467 1 Note that these motif descriptors are not the same as graph-set notation (Bernstein et al., 1995), but are a different notation developed to describe fully the type of motif and the sequence of individual interatomic contacts....
[...]

Journal Article•DOI•

Mercury: visualization and analysis of crystal structures

[...]

Clare F. Macrae¹, Paul R. Edgington¹, Patrick McCabe¹, Elna Pidcock¹, Greg P. Shields¹, Robin Taylor¹, Matthew Towler¹, Jacco van de Streek¹ - Show less +4 more•Institutions (1)

University of Cambridge¹

01 Jun 2006-Journal of Applied Crystallography

TL;DR: Mercury as discussed by the authors is a crystal structure visualization program that allows to display multiple structures simultaneously and overlay them, which can be used for comparison between crystal structures and to overlay them in a table or spreadsheets.

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Abstract: Since its original release, the popular crystal structure visualization program Mercury has undergone continuous further development. Comparisons between crystal structures are facilitated by the ability to display multiple structures simultaneously and to overlay them. Improvements have been made to many aspects of the visual display, including the addition of depth cueing, and highly customizable lighting and background effects. Textual and numeric data associated with structures can be shown in tables or spreadsheets, the latter opening up new ways of interacting with the visual display. Atomic displacement ellipsoids, calculated powder diffraction patterns and predicted morphologies can now be shown. Some limited molecular-editing capabilities have been added. The object-oriented nature of the C++ libraries underlying Mercury makes it easy to re-use the code in other applications, and this has facilitated three-dimensional visualization in several other programs produced by the Cambridge Crystallographic Data Centre.

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6,180 citations

"Mercury CSD 2.0 – new features for ..." refers background in this paper

...The most recent Mercury publication (Macrae et al., 2006) described the features added since the release of the original program....
[...]

Journal Article•DOI•

Retrieval of Crystallographically-Derived Molecular Geometry Information

[...]

Ian J. Bruno¹, Jason C. Cole, Magnus Kessler, Jie Luo, W. D. Sam Motherwell, Lucy H. Purkis, Barry Smith, Robin Taylor, Richard I. Cooper², Stephanie E. Harris, A. Guy Orpen - Show less +7 more•Institutions (2)

University of Cambridge¹, University of Oxford²

13 Oct 2004-Journal of Chemical Information and Computer Sciences

TL;DR: Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences.

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Abstract: The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution mat...

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799 citations

"Mercury CSD 2.0 – new features for ..." refers background in this paper

...Mogul A facility to check easily the intramolecular geometry of a molecule is now available....
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...The results of the comparison are presented in a datasheet view, with summary statistics of the Mogul distributions alongside a statistically based judgement as to whether the geometry in the original molecule is unusual or not....
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...Whole molecules or fragments of molecules can be compared with the Mogul (Bruno et al., 2004) libraries of bond lengths, bond angles and torsion angles....
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...In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar....
[...]

Journal Article•DOI•

IsoStar: A library of information about nonbonded interactions

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Ian J. Bruno¹, Jason C. Cole¹, Jos P. M. Lommerse¹, R. S. Rowland¹, Robin Taylor¹, Marcel L. Verdonk¹ - Show less +2 more•Institutions (1)

University of Cambridge¹

01 Nov 1997-Journal of Computer-aided Molecular Design

TL;DR: Crystallographic and theoretical data on intermolecular nonbonded interactions have been gathered together in a computerised library (’IsoStar‘) and show that there is great variability in the geometrical preferences of different types of hydrogen bonds.

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Abstract: Crystallographic and theoretical (ab initio) data on intermolecular nonbonded interactions have been gathered together in a computerised library ('IsoStar'). The library contains information about the nonbonded contacts formed by some 250 chemical groupings. The data can be displayed visually and used to aid protein-ligand docking or the identification of bioisosteric replacements. Data from the library show that there is great variability in the geometrical preferences of different types of hydrogen bonds, although in general there is a tendency for H-bonds to form along lone-pair directions. The H-bond acceptor abilities of oxygen and sulphur atoms are highly dependent on intramolecular environments. The nonbonded contacts formed by many hydrophobic groups show surprisingly strong directional preferences. Many unusual nonbonded interactions are to be found in the library and are of potential value for designing novel biologically active molecules.

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311 citations

"Mercury CSD 2.0 – new features for ..." refers background in this paper

...IsoStar contains data for intermolecular contacts taken from both small-molecule structures from the CSD and protein–ligand interactions in X-ray structures from the Protein Data bank (PDB)....
[...]
...IsoStar Intermolecular contacts can also be verified against a library of contact geometries encapsulated in the software IsoStar (Bruno et al., 1997)....
[...]
...In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar....
[...]
...An IsoStar scatter plot can be accessed from Mercury, by right-clicking on an atom of a functional group or a specific contact 468 Clare F. Macrae et al. Mercury CSD 2.0 J. Appl....
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...The intermolecular contact data within IsoStar are displayed as a three-dimensional scatter plot of the functional groups A and B of the contact....
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Journal Article•DOI•

COMPACK: a program for identifying crystal structure similarity using distances

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James A. Chisholm¹, James A. Chisholm², Sam Motherwell²•Institutions (2)

Pfizer¹, University of Cambridge²

01 Feb 2005-Journal of Applied Crystallography

TL;DR: In this article, the relative position and orientation of molecules are captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information, and can be used to determine whether two crystal structures are the same to within specified tolerances.

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Abstract: A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.

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293 citations

"Mercury CSD 2.0 – new features for ..." refers methods in this paper

...The similarity calculation method is derived from the program COMPACK (Chisholm & Motherwell, 2005) which analyses the geometry of a cluster of molecules, the default size of which is 15 molecules....
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